Phase-shifting locking is one of the key aspects of Scanning Beam Interference Lithography (SBIL) in achieving highly accurate exposure stitching of a large grating. To achieve this objective, a phase-shifting locking system was investigated for the stepping/scanning exposure trajectory of SBIL. Firstly, based on a previously proposed homodyne frequency-shifting interference pattern locking system and a heterodyne Littrow grating interferometer, a novel phase-shifting locking system scheme was proposed for SBIL. An experimental setup was then designed for this proposed scheme. Based on the setup, experimental and factor analyses were conducted to facilitate precise phase-shifting positioning control and an accuracy of ±3.27 nm (3σ, Λ=251 nm) was achieved. In addition, an accuracy of ±4.17 nm (3σ, Λ=251 nm) was achieved for phase-shifting locking control using a notch and PID control.